MolNFT v1 · #153178 · protein
Ligand-triggered allosteric ADP release primes a plant nlr complex
6J5W · RKS1: “Ligand-triggered allosteric ADP release primes a plant nlr complex”. Electron microscopy, 1 ligand (ADP), 16 pockets (best druggability 0.83). MolNFT v1 #153178 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6J5W
- Type
- protein
- Length
- 1,122 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RKS1; Disease resistance RPP13-like protein 4
- UniProt
- U5LSK3, Q38834
- Ligands
- ADP
- Pockets
- 16 · best druggability 0.83
Structure
electron microscopy · 2 distinct chains · 36% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | RKS1 | protein | 306 | 41% helix, 11% strand | U5LSK3 |
| A | Disease resistance RPP13-like protein 4 | protein | 816 | 34% helix, 10% strand | Q38834 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 962 | 0.83 | 0.84 | 118 | ADP |
| 2 | 1109 | 0.82 | 0.83 | 115 | empty |
| 3 | 92 | 0.78 | 0.99 | 22 | empty |
| 4 | 384 | 0.71 | 0.83 | 31 | empty |
| 5 | 50 | 0.68 | 0.97 | 16 | empty |
Interfaces
1 interface between chains.
- B–A · 2450 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 6J5W · Ligand-triggered allosteric ADP release primes a plant NLR complex · the same entry in another collection · chain B against B, TM-score 1.00
- Q38834 · AlphaFold monomer V2.0 prediction for disease resistance RPP13-like protein 4 (Q38834) · a predicted model of the same protein · chain A against A, TM-score 0.98
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt U5LSK3
- Every structure of UniProt Q38834
- Elsewhere: RCSB PDB 6J5W · PDBe 6J5W · UniProt U5LSK3 · UniProt Q38834
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